22-28785396-C-T

Position:

• chr22-28785396-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173510.4(CCDC117):​c.603-693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 151,922 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (602 hom., cov: 32)
• Consequence: CCDC117 NM_173510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

CCDC117 (HGNC:26599): (coiled-coil domain containing 117)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC117	NM_173510.4	c.603-693C>T		intron_variant		ENST00000249064.9
CCDC117	NM_001284263.2	c.549-693C>T		intron_variant
CCDC117	NM_001284264.2	c.378-693C>T		intron_variant
CCDC117	NM_001284265.1	c.207-693C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC117	ENST00000249064.9	c.603-693C>T		intron_variant		1	NM_173510.4	P1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11786 AN: 151802 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0723

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0777 AC: 11810 AN: 151922 Hom.: 602 Cov.: 32 AF XY: 0.0792 AC XY: 5879 AN XY: 74266

Gnomad4 AFR AF: 0.0992

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0633

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.0504

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0595 Hom.: 36

Bravo AF: 0.0833

Asia WGS AF: 0.175 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5997403; hg19: chr22-29181384;